Package org.broadinstitute.hellbender.metrics

Class PerUnitInsertSizeMetricsCollector

java.lang.Object

org.broadinstitute.hellbender.metrics.PerUnitInsertSizeMetricsCollector

All Implemented Interfaces:

Serializable, PerUnitMetricCollector<InsertSizeMetrics,Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs>

public final class PerUnitInsertSizeMetricsCollector
extends Object
implements PerUnitMetricCollector<InsertSizeMetrics,Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs>, Serializable

A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
PerUnitInsertSizeMetricsCollector(String sample, String library, String readGroup, double minimumPct, double deviations, Integer histogramWidth)

Method Summary

Modifier and Type	Method	Description
void	acceptRecord(org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs args)	Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
void	addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,Integer> file)	Any metrics collected will be added to the metric file provided.
PerUnitInsertSizeMetricsCollector	combine(PerUnitInsertSizeMetricsCollector sourceCollector)	Combine this PerUnitInsertSizeMetricsCollector with sourceCollector and return a combined PerUnitInsertSizeMetricsCollector.
void	finish()	When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
double	getTotalInserts()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

PerUnitInsertSizeMetricsCollector

public PerUnitInsertSizeMetricsCollector(String sample,
 String library,
 String readGroup,
 double minimumPct,
 double deviations,
 Integer histogramWidth)

Method Details

acceptRecord

public void acceptRecord(org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs args)

Description copied from interface: PerUnitMetricCollector

Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)

Specified by:

acceptRecord in interface PerUnitMetricCollector<InsertSizeMetrics,Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs>

Parameters:

args - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class

finish

public void finish()

Description copied from interface: PerUnitMetricCollector

When all records have been collected, compute any final values needed to finish constructing metrics/Histogram

Specified by:

finish in interface PerUnitMetricCollector<InsertSizeMetrics,Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs>

getTotalInserts

public double getTotalInserts()

addMetricsToFile

public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,Integer> file)

Description copied from interface: PerUnitMetricCollector

Any metrics collected will be added to the metric file provided.

Specified by:

addMetricsToFile in interface PerUnitMetricCollector<InsertSizeMetrics,Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs>

Parameters:

file - MetricsFile to which all metrics created by this collector should be added

combine

public PerUnitInsertSizeMetricsCollector combine(PerUnitInsertSizeMetricsCollector sourceCollector)

Combine this PerUnitInsertSizeMetricsCollector with sourceCollector and return a combined PerUnitInsertSizeMetricsCollector.

Parameters:

sourceCollector - PerUnitInsertSizeMetricsCollector to combine in

Returns:

PerUnitInsertSizeMetricsCollector representing the combination of the source collector with this collector